21-23085620-T-C

Variant names:

• chr21-23085620-T-C
• rs1506005
• ENST00000421604.1:n.297+17584T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421604.1(ENSG00000230972):​n.297+17584T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,046 control chromosomes in the GnomAD database, including 656 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.077 (656 hom., cov: 32)
• Consequence: ENSG00000230972 ENST00000421604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 1 publications found

Genes affected

ENSG00000230972 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230972	ENST00000421604.1	n.297+17584T>C		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11691 AN: 151928 Hom.: 654 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.0183

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0819

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0769 AC: 11697 AN: 152046 Hom.: 656 Cov.: 32 AF XY: 0.0749 AC XY: 5570 AN XY: 74328

African (AFR) AF: 0.154 AC: 6394 AN: 41482

American (AMR) AF: 0.0526 AC: 803 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0360 AC: 125 AN: 3468

East Asian (EAS) AF: 0.151 AC: 779 AN: 5174

South Asian (SAS) AF: 0.0333 AC: 161 AN: 4828

European-Finnish (FIN) AF: 0.0183 AC: 194 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0447 AC: 3037 AN: 67904

Other (OTH) AF: 0.0820 AC: 173 AN: 2110

Alfa AF: 0.0615 Hom.: 52

Bravo AF: 0.0849

Asia WGS AF: 0.0740 AC: 256 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.84
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1506005; hg19: chr21-24457942;